PFRMAT SS
TARGET T0449
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0449.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0449.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0449.t04.str2.rdb  (weight 1.54758)
METHOD T0449.t04.alpha.rdb  (weight 0.659012)
METHOD T0449.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0449.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0449.t2k.str2.rdb  (weight 1.54758)
METHOD T0449.t2k.alpha.rdb  (weight 0.659012)
METHOD These files were combined by translating their predictions into EHL
METHOD predictions with tables generated by compare-real, and then combining
METHOD those predictions with weights proportional to their mutual information
METHOD with the EHL alphabet.  The comments from the individual files follow.
METHOD
METHOD Comments from T0449.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0449
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	    7 (1 EBGHSTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0449.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 1138
METHOD
METHOD ============================================
METHOD Comments from T0449.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0449
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	    6 (1 EBGHTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0449.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 1138
METHOD
METHOD ============================================
METHOD Comments from T0449.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0449
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   13 (1 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0449.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 1138
METHOD
METHOD ============================================
METHOD Comments from T0449.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0449
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   11 (1 ABCDEFGHIST )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0449.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 1138
METHOD
METHOD ============================================
METHOD Comments from T0449.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0449
METHOD Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    5	   15
METHOD	    7	   15
METHOD	    9	   15
METHOD	   13	    7 (1 EBGHSTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0449.t2k-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1)
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 399
METHOD
METHOD ============================================
METHOD Comments from T0449.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0449
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    5	   15
METHOD	    7	   15
METHOD	    9	   15
METHOD	   13	    6 (1 EBGHTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0449.t2k-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1)
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 399
METHOD
METHOD ============================================
METHOD Comments from T0449.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0449
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    5	   15
METHOD	    7	   15
METHOD	    9	   15
METHOD	   13	   13 (1 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0449.t2k-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1)
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 399
METHOD
METHOD ============================================
METHOD Comments from T0449.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0449
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    5	   15
METHOD	    7	   15
METHOD	    9	   15
METHOD	   13	   11 (1 ABCDEFGHIST )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0449.t2k-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1)
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 399
METHOD
METHOD ============================================
MODEL 1
M C 0.87
D C 0.51
Y E 0.79
T E 0.85
I E 0.81
E E 0.53
N C 0.81
N C 0.86
M C 0.71
I E 0.77
K E 0.91
V E 0.92
V E 0.92
I E 0.87
S E 0.65
D C 0.60
H C 0.72
G C 0.55
A E 0.72
E E 0.88
I E 0.93
Q E 0.88
S E 0.92
V E 0.91
K E 0.86
S E 0.70
A C 0.80
H C 0.88
T C 0.78
D C 0.54
E E 0.70
E E 0.78
F E 0.78
M E 0.69
W E 0.52
Q C 0.59
A C 0.75
N C 0.82
P C 0.72
E C 0.66
I C 0.61
W C 0.64
G C 0.71
R C 0.78
H C 0.80
A C 0.74
P C 0.63
V E 0.63
L E 0.67
F E 0.61
P E 0.47
I C 0.56
V C 0.64
G C 0.72
R C 0.68
L C 0.67
K C 0.80
N C 0.89
D C 0.84
E E 0.51
Y E 0.83
T E 0.79
Y E 0.65
K C 0.88
G C 0.89
K E 0.59
T E 0.81
Y E 0.78
H E 0.63
L C 0.62
G C 0.72
Q C 0.69
H C 0.65
G C 0.61
F C 0.52
A C 0.52
R C 0.60
N C 0.75
A C 0.75
D C 0.65
F E 0.72
E E 0.83
V E 0.88
E E 0.84
N E 0.81
H E 0.63
T C 0.58
K C 0.83
E C 0.84
S E 0.63
I E 0.87
T E 0.91
F E 0.91
L E 0.89
L E 0.82
K E 0.57
D C 0.70
N C 0.89
E H 0.71
E H 0.76
T H 0.78
R H 0.69
K H 0.49
V C 0.60
Y C 0.78
P C 0.81
F C 0.73
K C 0.53
F E 0.83
E E 0.90
F E 0.92
R E 0.93
V E 0.93
N E 0.93
Y E 0.92
N E 0.92
L E 0.89
M E 0.61
N C 0.89
N C 0.90
L E 0.58
L E 0.90
E E 0.93
E E 0.93
N E 0.93
F E 0.93
S E 0.92
V E 0.91
V E 0.85
N E 0.55
K C 0.81
S C 0.89
D C 0.87
E C 0.83
T C 0.69
M C 0.71
I C 0.57
F E 0.59
G E 0.64
V E 0.60
G E 0.47
G C 0.55
H C 0.71
P C 0.64
G C 0.51
F E 0.47
N E 0.56
L C 0.60
P C 0.68
T C 0.75
D C 0.69
H C 0.67
G C 0.66
E C 0.50
N E 0.55
K E 0.48
E C 0.41
D C 0.50
F C 0.47
Y C 0.40
F C 0.38
D C 0.43
M C 0.50
H C 0.54
P C 0.47
S C 0.49
V C 0.53
T C 0.57
R C 0.59
V C 0.56
R C 0.54
I C 0.56
P C 0.58
L C 0.63
K C 0.69
D C 0.68
A C 0.68
S C 0.68
L C 0.66
D C 0.63
W C 0.64
N C 0.66
N C 0.62
R C 0.62
S C 0.64
L C 0.63
A C 0.62
P C 0.62
T C 0.62
D C 0.63
S C 0.60
L C 0.57
I C 0.53
A C 0.54
L C 0.57
S C 0.59
D C 0.59
D C 0.53
L C 0.53
F C 0.60
K C 0.59
D C 0.51
D H 0.50
A H 0.59
L H 0.57
I H 0.55
Y H 0.53
E H 0.49
L C 0.37
R C 0.59
G C 0.76
N C 0.79
D C 0.82
N C 0.74
K C 0.49
V E 0.77
S E 0.88
L E 0.89
R E 0.86
T E 0.71
D C 0.71
K C 0.85
N C 0.87
K C 0.84
F C 0.54
H E 0.84
V E 0.91
N E 0.92
V E 0.91
W E 0.84
T E 0.52
R C 0.81
D C 0.87
A C 0.79
P C 0.76
F E 0.51
V E 0.85
G E 0.91
I E 0.92
W E 0.87
S E 0.62
Q C 0.66
Y C 0.80
P C 0.82
K C 0.81
T C 0.85
D C 0.86
N C 0.79
Y E 0.57
V E 0.76
C E 0.78
I E 0.70
E C 0.52
P C 0.71
W C 0.77
W C 0.81
G C 0.82
I C 0.79
A C 0.69
D C 0.68
R C 0.61
D C 0.56
D C 0.61
A C 0.61
D C 0.57
G H 0.48
D H 0.58
L H 0.58
E H 0.50
H C 0.51
K C 0.69
Y C 0.73
G C 0.73
M C 0.52
N E 0.76
H E 0.80
L E 0.59
K C 0.81
P C 0.91
G C 0.92
K C 0.69
E E 0.77
F E 0.86
Q E 0.88
A E 0.89
G E 0.91
F E 0.92
S E 0.93
M E 0.92
T E 0.91
Y E 0.87
H E 0.58
S C 0.65
T C 0.81
T C 0.75
D C 0.72
E C 0.68
V C 0.64
K C 0.66
L C 0.62
E C 0.66
H C 0.81
H C 0.66
H C 0.65
H C 0.67
H C 0.78
H C 0.91
END